Variant report

Variant	rs6539190
Chromosome Location	chr12:105477278-105477279
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105476762..105478986-chr12:105499431..105503042,4	K562	blood:
2	chr12:105476808..105479481-chr12:105501524..105503382,3	K562	blood:

Variant related genes	Relation type
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1196798	0.80[ASN][1000 genomes]
rs1196811	0.80[ASN][1000 genomes]
rs1345096	0.98[ASN][1000 genomes]
rs17036705	1.00[EUR][1000 genomes]
rs17036728	1.00[EUR][1000 genomes]
rs2272491	1.00[EUR][1000 genomes]
rs2272494	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289773	1.00[EUR][1000 genomes]
rs2293642	1.00[EUR][1000 genomes]
rs2305047	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2374449	0.98[ASN][1000 genomes]
rs3763992	1.00[EUR][1000 genomes]
rs3794234	1.00[EUR][1000 genomes]
rs3794235	1.00[EUR][1000 genomes]
rs3817608	1.00[EUR][1000 genomes]
rs4964331	0.98[ASN][1000 genomes]
rs60387890	0.91[AFR][1000 genomes]
rs61005937	1.00[EUR][1000 genomes]
rs6539183	0.93[ASN][1000 genomes]
rs6539186	0.93[ASN][1000 genomes]
rs6539188	0.98[ASN][1000 genomes]
rs6539193	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.98[ASN][1000 genomes]
rs7132855	0.88[ASN][1000 genomes]
rs7299166	0.91[ASN][1000 genomes]
rs7299701	0.98[ASN][1000 genomes]
rs7302854	0.93[ASN][1000 genomes]
rs73395721	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963643	0.91[AFR][1000 genomes]
rs7963877	0.93[ASN][1000 genomes]
rs7973422	0.93[ASN][1000 genomes]
rs9788027	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105471000-105477400	Weak transcription	Aorta	Aorta
2	chr12:105475000-105478000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:105476200-105478000	Flanking Active TSS	Osteobl	bone
4	chr12:105476400-105477400	Enhancers	Fetal Brain Male	brain
5	chr12:105476400-105478200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:105476600-105477400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:105476600-105477400	Flanking Active TSS	NHLF	lung
8	chr12:105476600-105477600	Active TSS	NHEK	skin
9	chr12:105476600-105478600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr12:105476800-105477400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:105476800-105477400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:105476800-105477400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:105476800-105477400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:105476800-105477400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:105476800-105477400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:105476800-105477400	Enhancers	Left Ventricle	heart
17	chr12:105476800-105477600	Active TSS	Pancreas	Pancrea
18	chr12:105476800-105477800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr12:105476800-105477800	Flanking Active TSS	Fetal Brain Female	brain
20	chr12:105476800-105478000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr12:105476800-105478000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
22	chr12:105476800-105478000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr12:105476800-105478000	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr12:105476800-105478000	Flanking Active TSS	NH-A	brain
25	chr12:105476800-105478200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:105477000-105477400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:105477000-105477400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr12:105477000-105477400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:105477000-105477400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr12:105477000-105477400	Enhancers	Fetal Heart	heart
31	chr12:105477000-105477400	Bivalent Enhancer	Fetal Lung	lung
32	chr12:105477000-105477400	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr12:105477000-105477400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr12:105477000-105477600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:105477000-105477600	Flanking Active TSS	A549	lung
36	chr12:105477000-105477800	Active TSS	Colonic Mucosa	Colon
37	chr12:105477000-105478000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr12:105477000-105478000	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr12:105477000-105478800	Active TSS	Brain Angular Gyrus	brain
40	chr12:105477200-105477400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr12:105477200-105477400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:105477200-105477400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:105477200-105477400	Bivalent Enhancer	Primary B cells from cord blood	blood
44	chr12:105477200-105477400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
45	chr12:105477200-105477400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:105477200-105477400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:105477200-105477400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:105477200-105477400	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr12:105477200-105477400	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr12:105477200-105477400	Flanking Active TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links